title: Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size.
abstract: BACKGROUND
  Six nucleotide (nt) insertion in the 5'-noncoding region (NCR) of the nucleoprotein (NP) gene of Newcaslte disease virus (NDV) is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX.
  
  
  RESULTS
  In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates.
  
  
  CONCLUSIONS
  The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.
authors.affiliation: Key Laboratory of Animal Infectious Diseases, Yangzhou University, Yangzhou 225009, PR China.
authors.forename: Xusheng
authors.initials: X
authors.lastname: Qiu
authors.forename: Qing
authors.initials: Q
authors.lastname: Sun
authors.forename: Shuang
authors.initials: S
authors.lastname: Wu
authors.forename: Li
authors.initials: L
authors.lastname: Dong
authors.forename: Shunling
authors.initials: S
authors.lastname: Hu
authors.forename: Chunchun
authors.initials: C
authors.lastname: Meng
authors.forename: Yantao
authors.initials: Y
authors.lastname: Wu
authors.forename: Xiufan
authors.initials: X
authors.lastname: Liu
mesh_terms: D000818:Animals; D001483:Base Sequence; D002645:Chickens; D002681:China / Q000453:epidemiology; D016679:Genome, Viral; D005838:Genotype; D008969:Molecular Sequence Data; D009521:Newcastle Disease / Q000453:epidemiology / Q000821:virology*; D009522:Newcastle disease virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D019590:Nucleocapsid Proteins; D009698:Nucleoproteins / Q000235:genetics; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology; D017422:Sequence Analysis, DNA; D014760:Viral Fusion Proteins / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
chemical_list: D019590:Nucleocapsid Proteins; D009698:Nucleoproteins; D014760:Viral Fusion Proteins; D014764:Viral Proteins; C409209:nucleoprotein, Newcastle disease virus